Just did that
I drilled the c'balance tubes for my -12 flaperons a few days ago (with considerable trepidation). Results were fine (whew!). Here's the checklist I followed:
> Cleco'd up spar, nose ribs, stnls tube, nose skin, then used a drill to mark all hole locations;
> Secured un-cleco'd tube on the bench with a drill press vise at one end and a V-block at the other;
> Used only new, American made cobalt drill bits, each one good for about 8 to 10 holes;
> Used plenty of Boelube;
> Used a battery powered hand drill, slow speed and moderate, steady pressure;
> Once starting a hole, did not stop until it was done.
I admit this may be a touch of overkill, but I often find that's a good substitute for experience and/or remedy for ignorance. I'm sure you'll get other, more knowledgeable advice here as well.